Caenorhabditis remanei (Nematode) Assembly and Gene Annotation

NOTE: The genome sequence and annotation for this nematode are updated in Ensembl Metazoa infrequently. The data shown here corresponds with WormBase WS279. For the latest genome and annotation, please visit [WormBase ParaSite]https://parasite.wormbase.org/Caenorhabditis_remanei_prjna53967) (for an Ensembl-oriented view), or WormBase.

About Caenorhabditis remanei

C. remanei is a small, free-living roundworm found in decaying plant material especially compost, mushroom beds in Northern temperate regions. The worms feed on the bacteria and other micro-organisms associated with plant decay. The biology of C. remanei is similar to that of C. elegans, with a short generation time through four larval stages into an adult. C.remanei has both male and female adults unlike the hermaphroditic species such as C. elegans and C. briggsae. All three species are often found at the same site. C. remanei is frequently found associated with snails, slugs, millipedes, mites and pill bugs, which are presumed to transport worms, especially the dormant dauer stage, from one location to another, as with other Caenorhabditids.

C. remanei was known as C. vulgaris prior to the demonstration that this was a junior synonym of C. remanei in 1996 (Sudhaus & Kiontke, 2006). The sequenced strain PB4641 was derived from a wild isolate EM464 isolated from a pillbug (Armadillidium vulgare) in Brooklyn, New York in 1990. The wild isolate was inbred for 20 generations in the lab of Scott Baird by transferral of a single gravid female per generation.

• C. remanei data at WormBase
• C. remanei data at WormBase ParaSite
• Roundworm Genome Sequencing white paper

Assembly

The C. remanei genome has been sequenced by the Genome Institute at Washington University as part of a larger NHGRI funded Roundworm Genome Sequencing project to expand the Caenorhabditis clade. The genome is approximately 450 Mb in size, considerably larger than that of the model Rhabditid C. elegans. The assembly has been performed using PCAP.

Annotation

Genome annotation was undertaken by the WormBase group based in part on the high quality C. elegans annotations and guided by the nGASP assessment project (Coghlan et al, 2008). Since then, many gene structures have been improved manually by WormBase curators. The annotation here corresponds with WormBase WS279.

References

1. Ecology of Caenorhabditis species.
   Kiontke K, Sudhaus W. 2006. WormBook. :1-14.
2. nGASP--the nematode genome annotation assessment project.
   Coghlan A, Fiedler TJ, McKay SJ, Flicek P, Harris TW, Blasiar D, nGASP Consortium, Stein LD. 2008. BMC Bioinformatics. 9:549.

Links

• C. remanei data at WormBase
• C. remanei data at WormBase ParaSite